George A O'Toole threw out a gagging order imposed on the academics by the Massachusetts Bay Transportation Authority (MBTA), which had claimed that the data breach put its operations in danger.
The three students had previously boasted in a presentation that they had "hacked" the subway payment system using computers.
During the talk, they had tantalised their audience with the suggestion that their findings could provide them with "free subway rides for life".
Their hacking work had already been submitted in class at MIT - receiving an "A" grade from math professor Ronald Rivest.
Cindy Cohn, the students' attorney, commented: "The MBTA ultimately is trying to silence some uncomfortable truths that these students uncovered."
She added: "They brought an action against three college kids rather than address the problems in their own house."
Following the students hack, the MBTA has admitted to security flaws in its card system.